Overcoming Species Boundaries in Peptide Identification with Bayesian Information Criterion-driven Error-tolerant Peptide Search (BICEPS)

A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics

(2011) Jing Li et al.   MOLECULAR & CELLULAR PROTEOMICS

Genome Assembly Has a Major Impact on Gene Content: A Comparison of Annotation in Two Bos Taurus Assemblies

(2011) Liliana Florea et al.   PLoS One

Estimating the Confidence of Peptide Identifications without Decoy Databases

(2010) Bernhard Y. Renard et al.   ANALYTICAL CHEMISTRY

TagRecon: High-Throughput Mutation Identification through Sequence Tagging

(2010) Surendra Dasari et al.   JOURNAL OF PROTEOME RESEARCH

Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy

(2009) Xiaowen Liu et al.   BIOINFORMATICS

Tools for exploring the proteomosphere

(2009) Andrej Shevchenko et al.   Journal of Proteomics

Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications forde NovoPeptide Sequencing and Identification

(2009) Sangtae Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

When less can yield more - Computational preprocessing of MS/MS spectra for peptide identification

(2009) Bernhard Y. Renard et al.   PROTEOMICS

Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. canadensis

(2009) M. H. Schweitzer et al.   SCIENCE

Proteome-Wide Identification of Proteins and Their Modifications with Decreased Ambiguities and Improved False Discovery Rates Using Unique Sequence Tags

(2008) Yufeng Shen et al.   ANALYTICAL CHEMISTRY

De Novo Sequencing of Unique Sequence Tags for Discovery of Post-Translational Modifications of Proteins

(2008) Yufeng Shen et al.   ANALYTICAL CHEMISTRY

A Hybrid Method for Peptide Identification Using Integer Linear Optimization, Local Database Search, and Quadrupole Time-of-Flight or OrbiTrap Tandem Mass Spectrometry

(2008) Peter A. DiMaggio et al.   JOURNAL OF PROTEOME RESEARCH

DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring

(2008) David L. Tabb et al.   JOURNAL OF PROTEOME RESEARCH

Protein identification pipeline for the homology-driven proteomics

(2008) Magno Junqueira et al.   Journal of Proteomics

Automated de novo protein sequencing of monoclonal antibodies

(2008) Nuno Bandeira et al.   NATURE BIOTECHNOLOGY

Climate Change Goals: Where to Begin?

(2008) B. D. Goldstein et al.   SCIENCE

Comment on "Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry"

(2008) P. A. Pevzner et al.   SCIENCE

Computational Methods for Protein Identification from Mass Spectrometry Data

(2008) Leo McHugh et al.   PLoS Computational Biology